Exploring Environmental DNA (eDNA) to Assess Biodiversity of Hard Substratum Faunal Communities on the Lucky Strike Vent Field (Mid-Atlantic Ridge) and Investigate Recolonization Dynamics After an Induced Disturbance

Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?

“…Less effort has been devoted to the study of hard-substrate natural benthic communities. These have been analysed either using indirect methods based on deploying artificial substrates (Cahill et al, 2018;Leray & Knowlton, 2015;Pearman et al, 2019;Ransome et al, 2017), or by directly taking samples by scraping off standardized surfaces (Shum, Barney, O'Leary, & Palumbi, 2019;Wangensteen, Cebrian, Palacín, & Turon, 2018;Wangensteen, Palacín, Guardiola, & Turon, 2018) or using suction devices (Cowart et al, 2020;De Jode et al, 2019).…”

Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

“…Two broad approaches that have received the most attention in eDNA-based studies are barcoding and metabarcoding. The main difference between barcoding and metabarcoding is that barcoding uses species-specific primers to detect the DNA fragments of a single species within an environmental sample Franklin et al 2019;Strickland & Roberts 2019;Akamatsu et al 2020;Harper et al 2020;Kessler et al 2020;Togaki et al 2020) while metabarcoding uses universal primers to simultaneously detect millions of DNA fragments from the widest possible range of species from multiple trophic levels and domains of life (Alexander et al 2020;Cowart et al 2020;Djurhuus et al 2020;Yang & Zhang 2020;Zhang et al 2020b).…”

“…Sequence filtering is a routine process in eDNA analysis and occurs at multiple steps of the bioinformatics pipeline. For metabarcoding, raw sequence data are initially processed to filter and correct (where possible) low-quality and erroneous reads (Valentini et al 2016a;Evans et al 2017a;Günther et al 2018;Bakker et al 2019;Rytkonen et al 2019;Cowart et al 2020;Zhang et al 2020a). This quality control step removes any phiX reads (common in marker gene sequencing) and chimeric sequences detected in the raw sequencing data.…”

“…Traditional surveys are also generally labor intensive and time consuming, and can be inefficient at detecting the true biodiversity present (van der Heyde et al ;Basset et al 2012;Gómez-Zurita et al 2016;Stoeckle et al 2016;Evans et al 2017b;Rodriguez-Estrella et al 2019;Zhang et al 2020b). The advent of rapid and relatively cheap DNA sequencing techniques has significantly enhanced biodiversity research by overcoming some of the challenges of labor-intensive traditional surveys and offering the opportunity to efficiently characterize biodiversity in time and space, using standardized methods (Corlett 2017;Alexander et al 2020;Cowart et al 2020;Ji et al 2020;Leempoel et al 2020;Sales et al 2020;Yang & Zhang 2020). Among these techniques, environmental DNA (eDNA) sampling has attracted worldwide attention, and interest in using this tool for biodiversity assessment has grown rapidly in the past few years (Figure 1).…”

Strengthening marine amphipod DNA barcode libraries for environmental monitoring

“…Environmental DNA (eDNA) barcoding technology is finding innovative applications for monitoring marine biodiversity (Nguyen et al, 2020), from deep sea hydrothermal vents (Cowart et al, 2020) to plankton gut materials (Oh et al, 2020) and also in tracking terrestrial biodiversity (Heyde et al, 2020). eDNA barcoding technology has also been shown to be useful in monitoring the ecosystem to detect invasive species (Kim et al, 2020) from the DNA extracted from marine litters (Ibabe et a;.…”